That's the message from this week's congressional hearing on protections for national security whistle-blowers - the first in more than a decade. "The system is broken," says Rep. Christopher Shays (R) of Connecticut, who chaired the House Government Affairs subcommittee hearing.

Disclosures of flawed prewar intelligence, secret prisons and prisoner abuse, and warrantless surveillance by the National Security Agency have launched a debate on the conduct of the war on terror within Congress and the American public. Critics say some of those disclosures also compromised national security.

"At the Central Intelligence Agency, we are more than holding our own in the global war on terrorism, but we are at risk of losing a key battle: the battle to protect our classified information," wrote CIA director Porter Goss in The New York Times last Friday.

The struggle over dissent in dangerous times is not confined to national security matters, however. It appears to be settling deeper into the federal bureaucracy, where government scientists and even analysts at the scholarly Congressional Research Service - who are not actually blowing any whistles but who are staking out positions that deviate from the administration's - report efforts to control their contact with the press and public.

If whistle-blowers and others "do not see an option for dissent within the system, then the system is in bad shape," says Steven Aftergood, director of the Project on Government Secrecy at the Federation of American Scientists. "Secrecy has become a growth industry.... It makes it harder for ordinary citizens ... to ask questions ... and to hold officials accountable."

The lips-stay-sealed climate is felt most acutely, at least these days, by those in national-security fields. Indeed, a Justice Department investigation is under way to discover who divulged the existence of warrantless eavesdropping by the NSA - a probe that may yield criminal charges against the individuals responsible.

Richard Levernier is one who went public with his security concerns - and feels he's paid a heavy price. He first reported security breaches at the Department of Energy's nuclear weapons sites to management. Seeing no changes, he released an unclassified report to the media. While government investigators found his concerns credible, he lost his security clearance. Four years later, he's unemployed and, he says, unemployable.

"I spent my whole life in the nuclear security business. And you can't get a key to the men's room without a clearance," says Mr. Levernier, one of five whistle-blowers who spoke Tuesday before the Subcommittee on National Security, Emerging Threats, and International Relations.

Army Spc. Samuel Provance was demoted after disobeying an order not to speak to the press about prisoner mistreatment at Abu Ghraib in Iraq. "Young soldiers were scapegoated, while superiors misrepresented what had happened.... I was ashamed and embarrassed to be associated with it," he told the House panel.

Lt. Col. Anthony Shaffer lost his security clearance after testifying to the 9/11 Commission and Congress about Operation Able Danger, a program that he says tagged four 9/11 hijackers before the attacks.

Former FBI special agent Michael German and former intelligence officer Russell Tice also testified that they felt they'd been retaliated against for speaking out about problems, and both lost their security clearances.

"Security clearance revocation is the new harassment of choice against national security workers," says Thomas Devine, legal director for the Government Accountability Project, a nonprofit public-interest law firm in Washington that assists whistle-blowers.

While federal workers have had whistle-blower protection since 1989, a 1999 US court ruling requires these workers to have irrefutable evidence of waste, fraud, or abuse to be eligible for protection. Last year, House and Senate committees each passed bills that strengthened protections for whistle-blowers, but neither bill has come to the floor for a vote. Only the Senate version includes national security whistle-blowers.

Outside the realm of national security, James Hansen, the top climate scientist at NASA, spoke out about efforts by the NASA press office to screen his speeches and limit his contact with the press.

In response, Rep. Sherwood Boehlert (R) of New York, chairman of the House Science Committee, backed Dr. Hansen. "Good science cannot long persist in an atmosphere of intimidation," he wrote to NASA administrator Michael Griffin. Mr. Griffin e-mailed all NASA employees, affirming that staff should not alter, filter, or adjust scientific work.

But Hansen says the issue is not yet resolved, citing a pending investigation by the House Energy and Commerce Committee challenging the scholarship of other scientists working on global warming.

When lawmakers on the House panel asked what other issues they should heed, watchdog groups cited the case of Louis Fisher, a senior analyst at Congressional Research Service.

His office door is papered with book jackets from his works, many of them on congressional-executive relations. When Mr. Fisher spoke publicly about a report he wrote on national security whistle-blowers, CRS managers warned him not to take positions on issues before Congress.

"CRS researchers are instructed from the time they're hired that their role is an educative one, not an advocative one," Daniel Mulhollan, CRS director, wrote in an e-mail statement. "If CRS is to serve all members of Congress ... it must be understood to be equally valuable to those on competing sides of an issue."

The warning set off protests from political scientists and public-interest groups. "The CRS has been severely compromised," says William Weaver, a political scientist at the University of Texas in El Paso and a founder of the National Security Whistle-blowers Coalition.

Says Fisher himself: "For the last 33 years my job was to defend legislative prerogative and constitutional government, and suddenly that's a bad thing to do. There are mixed signals inside this [CRS] house. People are hunkered down."